tbuckley/cabot-search huggingface dataset:
Abstract B009: Establishing new cell lines from undifferentiated pleomorphic sarcoma for sarcoma research
Authors: Hye Jin You, Eun-Young Lee, Abu Rayhan, Hyun Guy Kang, June Hyuk Kim, Jongwoong Park
Journal: Clinical Cancer Research (2022)

Abstract Undifferentiated pleomorphic sarcoma (UPS), also known as malignant fibrous histiocytoma (MFH), is a high-grade soft-tissue sarcoma (STS). Despite of importance, there are very few models for study. Here, we have established and characterized UPS-derived cell lines. Cells were obtained UPS tissues by mincing followed by extracting or dissociating using enzymes and cultured by regular culture environment. Cells were maintained and immortal for months without artificial treatment and tumorigenic in vivo study. The tissues from in vivo study and tissues from patients were compared if it is representative for UPS by immunohistochemistry. Transcriptome from tissues and cell lines were compared. Several genes were identified as specific in tumor tissues and cell lines. Fusion genes were also identified. This study showed that new UPS cell lines might be a good resource for UPS study to get new insights. Citation Format: Hye Jin You, Eun-Young Lee, Abu Rayhan, Hyun Guy Kang, June Hyuk Kim, Jongwoong Park. Establishing new cell lines from undifferentiated pleomorphic sarcoma for sarcoma research [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr B009.
Abstract IA025: Using genetically engineered mouse models to study sarcoma metastasis
Authors: David G. Kirsch, Rutulkumar Patel, Sophie R. Finkelstein, Joy Ban, Yuning J Tang, Jianguo Huang, Benjamin A. Alman, Yvonne M. Mowery
Journal: Clinical Cancer Research (2022)

Abstract Despite aggressive conventional therapy, many patients with high-risk soft-tissue sarcoma develop metastatic disease. To investigate mechanism(s) of sarcoma metastasis, our lab has utilized genetically engineered mouse models. For example, we injected an adenovirus expressing Cre recombinase (adeno-Cre) into the gastrocnemius muscle of LSL-KrasG12D; p53Flox/Flox (KP) mice to initiate high grade undifferentiated pleomorphic sarcomas, and after amputation approximately 40% of the mice develop lung metastasis. Using a genetic approach, we found that miR-182, NEAT-1, and HIF-1a regulate metastasis to the lung. We also performed lineage tracing with complementary fluorescent proteins and CRISPR-generated bar codes to find that lung metastases from KP sarcomas arise from clones with specific gene expression profiles. Although the KP sarcoma model is useful for studying metastasis, one limitation of this model is that there are few non-synonymous mutations to engage the immune system. Therefore, we generated a high mutational load primary mouse model of soft tissue sarcoma by injecting adeno-Cre into the gastrocnemius muscle of p53Flox/Flox mice to delete p53 and also injected 3-methylcholanthrene (MCA) to generate primary p53/MCA undifferentiated pleomorphic sarcomas. In this p53/MCA model, the overall rate of lung metastasis after amputation was surprisingly low (~12%). We hypothesized that the immune system suppressed lung metastasis in this model. However, when we generated p53/MCA sarcomas in Rag2 −/− mice that lack mature B and T cells, we still observed a low rate of lung metastasis after amputation. These data suggest that mutations caused by MCA may have disabled tumor intrinsic factors needed to drive sarcoma metastasis. We are currently performing genome-wide screens in the p53/MCA model to search for genes required for sarcoma metastasis. Citation Format: David G. Kirsch, Rutulkumar Patel, Sophie R. Finkelstein, Joy Ban, Yuning J Tang, Jianguo Huang, Benjamin A. Alman, Yvonne M. Mowery. Using genetically engineered mouse models to study sarcoma metastasis [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA025.
Abstract IA020: Reprogramming of myogenic transcription factors in rhabdomyosarcoma
Authors: Heide L. Ford, Jessica Y. Hsu, Etienne P. Danis, Stephanie Nance, Jenean H. O’Brien, Annika L. Gustafson, Veronica M. Wessells, Andrew E. Goodspeed, Jared C. Talbot, Sharon L. Amacher, Paul Jedlicka, Joshua C. Black, James C. Costello, Adam D. Durbin, Kristin B. Artinger
Journal: Clinical Cancer Research (2022)

Abstract Rhabdomyosarcoma, a pediatric malignancy with partial resemblance to undifferentiated skeletal muscle, is characterized by high expression of myogenic-lineage transcription factors such as MYOD1 and MYOG. Despite high expression of these transcription factors, which in normal muscle result in differentiation, RMS cells fail to differentiate, suggesting the presence of factors that inhibit their normal differentiation-promoting functions. In this talk, I will present data that the key muscle transcriptional regulator, SIX1, which in development activates the myogenic regulatory factors (MRFs) and promotes muscle differentiation, in fact inhibits differentiation in fusion-negative (FN) RMS. SIX1 holds FN-RMS cells in a progenitor-like state by altering the chromatin landscape and causing MYOD1, a key MRF, to preferentially bind to regulatory regions of genes permissive to growth rather than differentiation. Loss of SIX1 results in re-localization of MYOD1 to promoters/enhancers of genes associated with differentiation, and further results in increased binding of MYOG at such loci. Altered binding of MYOD1 and MYOG in response to SIX1 loss results in marked inhibition of RMS growth in vivo, via induction of differentiation. These data suggest that SIX1 acts as a master regulatory factor controlling the fate of RMS cells. Data will be presented that suggest dynamic actions of SIX1 and its co-factors throughout normal muscle differentiation, whereby high levels of SIX1 expressed in early muscle differentiation may mimic a transcriptional state seen in RMS. We hypothesize that the specific levels of SIX1, combined with a unique combination of transcriptional co-factors, reprogram genome-wide binding of MRFs to different promoter/enhancer sites at specific developmental time points, and that RMS is trapped in an early developmental state where SIX1 represses differentiation via genome-wide alterations in MRF binding that favor growth. Understanding the co-factors that work with SIX1 to alter chromatin state and MRF binding may enable the discovery of novel targets whose inhibition could serve as a relatively non-toxic treatment to restore normal developmental processes and inhibit RMS progression. Citation Format: Heide L. Ford, Jessica Y. Hsu, Etienne P. Danis, Stephanie Nance, Jenean H. O’Brien, Annika L. Gustafson, Veronica M. Wessells, Andrew E. Goodspeed, Jared C. Talbot, Sharon L. Amacher, Paul Jedlicka, Joshua C. Black, James C. Costello, Adam D. Durbin, Kristin B. Artinger. Reprogramming of myogenic transcription factors in rhabdomyosarcoma [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA020.
Abstract A007: Resident memory T cells express PD-1 in high grade liposarcoma
Authors: Christina V. Angeles, Jichang Han, Jodi Wilkoswki, Scott Bresler
Journal: Clinical Cancer Research (2022)

Abstract Objective: Memory T cells play crucial roles in anti-tumor immunity. Tumor-associated resident memory T cells (TRM) have been associated with durable immune response and improved patient survival across multiple tumor types. SARC028, a phase II, multicenter trial of pembrolizumab, a programmed death 1 (PD-1) checkpoint inhibitor immunotherapy, showed promising activity in select histologic subtypes of advanced soft tissue sarcoma (STS), including dedifferentiated liposarcoma (DDLPS). However, there was only a 20% overall response rate. Notably, the patients who did respond to immunotherapy had durable responses, supporting our enthusiasm to understand the potential role for TRM in liposarcoma anti-tumor immunity. The characterization of memory T cells in liposarcoma, and whether TRM are present has not been explored. Design: Fresh retroperitoneal liposarcoma specimens from 8 patients: 3 well-differentiated liposarcoma (WDLPS) and 5 DDLPS were collected. Lymphocytes were analyzed by flow cytometry using T-cell (CD45, CD3, CD4, CD8) and phenotypic markers (CD69, CD62L, CD103, CD49a, PD-1, TIM-3). Results: DDLPS had a 4-fold higher overall T-cell infiltration and a 2.5-fold higher CD8+/CD4+ T-cell ratio than WDLPS. DDLPS contained CD8+ T cells with a CD45RA− CCR7− CD69hi CD62Llo phenotype, characteristic of a TRM response, and well as CD69lo effector memory T (TEM) cells. DDLPS had 3-fold more TRM than WDLPS. DDLPS had a much higher level of activated PD-1+ CD69+ CD8+ resident memory T-cell population compared to WDLPS. Additionally, the population of TRM had higher PD-1 expression compared to TEM in both DDLPS and WDLPS. Conclusions: These data suggest that TRM subsets may contribute to the responsiveness to anti-PD1 therapy in patients with DDLPS. Further investigations may lead to the discovery of TRM-targeted T-cell therapies in DDLPS, which currently has limited treatment options. Citation Format: Christina V. Angeles, Jichang Han, Jodi Wilkoswki, Scott Bresler. Resident memory T cells express PD-1 in high grade liposarcoma [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr A007.
Abstract IA007: B cell immunity generation in tertiary lymphoid structures, a major determinant of sarcoma immune response to immunotherapy
Authors: Wolf H. Fridman
Journal: Clinical Cancer Research (2022)

Abstract The presence of tertiary lymphoid structures (TLSs) and a high intratumoral density of B lymphocytes have been associated with improved survival in several tumor types. We investigated the impact of TLS on responses to immunotherapy and, analyzing a large-scale retrospective analysis of three independent cohorts of patients with cancer, including sarcomas, who were treated with anti-PD-1 or anti-PD-L1 antibodies, we showed that the presence of mature TLSs was associated with improved objective response rates, progression-free survival and overall survival, independent of PD-L1 expression status and CD8+T cell density. To decipher the role of B cells in such responses, we performed spatial transcriptomics and examined the nature of B cell responses within TLS structure. B cells were enriched in TLS, and therein we could identify all B cell maturation stages toward plasma cell (PC) formation. B cell repertoire analysis revealed clonal diversification, selection, expansion in TLS and the presence of full mature clonotypes at distance. In TLS+ tumors, IgG producing PCs disseminated into the tumor beds along fibroblastic tracks. TLS+ tumors exhibited high frequencies of IgG-producing PCs and IgG-stained and apoptic malignant cells, suggestive of anti-tumor effector activity. We validated these findings in a prospective trial in metastatic Soft Tissue Sarcoma (STS) bearing patients. PEMBROSARC is a multi-cohort phase II study of pembrolizumab combined with low-dose cyclophosphamide in patients with advanced STS. The 6-months non-progressive rate (NPR) and the objective response rates previously reported in cohorts including all comers were 4.9% and 2.4%, respectively. In the cohort enrolling patients selected based on the presence of TLS, the 6-month NPR was 40% and the objective response rate was 30%. Exploratory analyses reveled that infiltration by IgG antibody-producing plasma cells was associated with improved clinical outcome as well as the presence of IgG antibodies on tumor cells. Altogether, these results establish that maturation, selection and amplification of B cells in intratumoral TLSs results in Plasma Cells generation which may produce anti-tumor antibodies. The latter may amplify in situ antitumor immune responses leading to better therapeutic responses to immunotherapy. Citation Format: Wolf H. Fridman. B cell immunity generation in tertiary lymphoid structures, a major determinant of sarcoma immune response to immunotherapy [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA007.
Abstract A037: TT-00420, a novel kinase inhibitor potentially benefiting c-Myc amplified/overexpressed osteosarcoma
Authors: Yingqi Hua, Xiaoyan Qiang, Kai Tian, Yafei Jiang, Frank Wu, Peng Peng
Journal: Clinical Cancer Research (2022)

Abstract Osteosarcoma (OS) is the most common bone tumor in pediatric patients, whose effective therapies are of great unmet medical needs, particularly for those of high-risk features. c-Myc, a well-known oncogene, is commonly amplified/overexpressed in OS patients, contributes to dismal prognosis and associates with lower 5-year overall survival rate, which is also confirmed by our retrospective analysis for the correlation between c-Myc gene amplification/overexpression and patient prognosis in our patient cohort. TT-00420, a clinical-stage small molecule targeting Aurora A/B, VEGFRs, FGFRs, JAKs and CSF1R, has demonstrated down-regulation on c-Myc expression in TNBC studies. Moreover, as reported, Aurora kinases and c-Myc regulate each other back and forth, triggering maintenance of the malignant state. In this study, we examined the efficacy of TT-00420 in c-Myc-amplified/overexpressed OS. In pre-clinical clonogenic assay, TT-00420 significantly inhibited the colony formation in c-Myc-overexpressed OS cell lines in a dose-dependent manner. In MNNG/HOS cell line, we demonstrated that TT-00420 dramatically suppressed Aurora kinase pathway and blunted c-Myc protein expression level, indicating TT-00420 might down-regulate c-Myc by Aurora kinases inhibition. In pre-clinical in-vivo efficacy studies, 143B cells were injected into the medullary cavity of the tibia to make the orthotopic OS xenograft model. With 15 mg/kg/day treatment of TT-00420, tumor growth was obviously inhibited as compared to vehicle group. Immunohistochemistry (IHC) analyses in tumors revealed that TT-00420-treated tumors exhibited increased apoptosis with upregulated expression of cleaved caspase 3 (CC3) and H2AX, and significantly decreased proliferations with raised expression of Ki67. Moreover, in a c-Myc-overexpressed OS patient-derived xenograft (PDX) model from a male pediatric patient, 15 mg/kg/day TT-00420 dramatically blunted the tumor growth with a TGI of 87.6%. In China, an investigator-initiated trial is currently ongoing to evaluate the safety and tolerability of TT-00420 in OS patients with c-Myc overexpression (ChiCTR2000036618). Taken together, TT-00420 depicted robust anti-tumor activity in c-Myc overexpressed OS both in vitro and in vivo with downregulation of c-Myc expression, indicating its potential as a novel monotherapy for OS patients with c-Myc overexpression. Future clinical trial result is of great expectation. Citation Format: Yingqi Hua, Xiaoyan Qiang, Kai Tian, Yafei Jiang, Frank Wu, Peng Peng. TT-00420, a novel kinase inhibitor potentially benefiting c-Myc amplified/overexpressed osteosarcoma [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr A037.
Abstract B021: Long non-coding RNAs that are required for robust cell growth in ewing Sarcoma
Authors: Marcela C. Briones Martin del Campo, Alex Lee, Max Horlbeck, Truc Dinh, Marta Roman-Moreno, Leanne Sayles, Bokyung Seong, Kimberly Stegmaier, Luke Gilbert, E. Alejandro Sweet-Cordero
Journal: Clinical Cancer Research (2022)

Abstract While long non-coding RNAs (lncRNAs) are upregulated in many cancers, their role in pediatric cancers is unclear. Among pediatric cancers, Ewing sarcoma is unique in that these tumors show upregulation of a large, specific number of lncRNAs. To perform an unbiased screen of lncRNA function in Ewing sarcoma, we used a pooled CRISPRi screen to identify lncRNAs that modify cell growth. We included in the pooled library lncRNAs either highly expressed in Ewing Sarcoma or directly regulated by the driving oncogene in Ewing Sarcoma, EWS-FLI. We identified 49 lncRNAs that when inhibited by CRISPRi led to decreased growth of Ewing cell lines. Among those that scored most significantly were the small nucleolar host genes SNHG1, SNHG12, and SNHG30. To validate the screening results, we individually cloned the two most depleted sgRNAs targeting for each of these three lncRNAs into a lentiviral vector. We expressed these sgRNAs in three different dCas9-KRAB+ Ewing cell lines and used internally controlled growth assays to test whether the observed phenotypes from the screens were reproducible. We confirmed that for all three lncRNAs hits significantly affected Ewing’s growth, and their depletion leads to an increase in apoptosis. To determine how lncRNAs influence the ability of Ewing sarcoma cells to growth and survive in vivo, we performed a subcutaneous xenograft CRISPRi screen using the same pooled library used in vitro. The lncRNAs with the strongest pro-growth phenotype after knock-down were PVT1 and the uncharacterized LINC02688. Ongoing studies are directed at determining the Ewing-specific role of these lncRNAs. Overall, our studies demonstrate the value of studying lncRNA functions in vitro and in vivo, provides a valuable resource of new lncRNAs targets to further research and establishes a framework for systematic discovery of functional lncRNAs in Ewing cells. Citation Format: Marcela C. Briones Martin del Campo, Alex Lee, Max Horlbeck, Truc Dinh, Marta Roman-Moreno, Leanne Sayles, Bokyung Seong, Kimberly Stegmaier, Luke Gilbert, E. Alejandro Sweet-Cordero. Long non-coding RNAs that are required for robust cell growth in ewing Sarcoma [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr B021.
Abstract PR011: Characterization of the precancerous and cancer microenvironment in a zebrafish sarcoma model
Authors: Heather R. Shive, John S. House, Jordan L. Ferguson, Dereje D. Jima, Aubrie A. Selmek, Dillon T. Lloyd
Journal: Clinical Cancer Research (2022)

Abstract Contributions of the microenvironment to soft tissue sarcoma progression are relatively undefined, representing a major impediment to identifying essential regulatory networks in sarcomagenesis. Furthermore, genetic and molecular characteristics that distinguish precancerous versus cancerous microenvironments are not well known across human cancer types. While animal models have the potential to reveal these complex processes, significant impediments to such inquiries include (1) the difficulty in distinguishing microenvironmental cells from precancerous or cancer cells in tissue specimens; and (2) the challenge in defining a discrete tissue with known cancer predilection that represents a precancerous microenvironment. We developed a unique zebrafish model that allows segregation of microenvironmental, precancerous, and cancerous cell populations by fluorescence-activated cell sorting. This model exhibits high predilection for malignant peripheral nerve sheath tumor (MPNST), a type of soft tissue sarcoma with a particularly poor prognosis due to aggressive growth, limited response to conventional treatment, and ineffective targeted therapy options. Using RNA-seq, we profiled the transcriptomes of microenvironmental cells from our zebrafish MPNST model and determined that the precancerous and cancerous microenvironments exhibit broad activation of inflammatory and immune-associated signaling networks. Markers for both M1 and M2 macrophage polarization were upregulated in precancerous and cancerous microenvironments, suggesting the presence of a mixed macrophage population during sarcomagenesis. Patterns of ligand and receptor expression based on a previously defined human ligand-receptor network identified significant upregulation of multiple tumor-promoting ligands in both precancerous and cancerous microenvironments. We also identified specific ligand-receptor pairs that may mediate key signaling events during sarcoma initiation and progression. Together this work provide new insight into distinguishing characteristics of the cancer-prone cellular microenvironment that may promote MPNST initiation and progression in vertebrates. Citation Format: Heather R. Shive, John S. House, Jordan L. Ferguson, Dereje D. Jima, Aubrie A. Selmek, Dillon T. Lloyd. Characterization of the precancerous and cancer microenvironment in a zebrafish sarcoma model [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr PR011.
Abstract IA017: Impact of oxygen and nutrient availability on sarcoma tumor neighborhood
Authors: M. Celeste Simon
Journal: Clinical Cancer Research (2022)

Abstract Molecular oxygen (O2) sustains intracellular bioenergetics and is consumed by numerous biochemical reactions, making it essential for most species on Earth. Accordingly, decreased oxygen concentration (hypoxia) is a major stressor that generally subverts life of aerobic species and is a prominent feature of pathological states encountered in bacterial infection, inflammation, wounds, cardiovascular defects and cancer. Therefore, key adaptive mechanisms to cope with hypoxia have evolved in mammals. Systemically, these adaptations include increased ventilation, cardiac output, blood vessel growth and circulating red blood cell numbers. On a cellular level, ATP- consuming reactions are suppressed, and metabolism is altered until oxygen homeostasis is restored. A critical question is how mammalian cells sense oxygen levels to coordinate diverse biological outputs during hypoxia. The best- studied mechanism of response to hypoxia involves hypoxia inducible factors (HIFs), which are stabilized by low oxygen availability and control the expression of a multitude of genes, including those involved in cell survival, angiogenesis, glycolysis and invasion/metastasis. Importantly, changes in oxygen can also be sensed via other stress pathways as well as changes in metabolite levels and the generation of reactive oxygen species by mitochondria. Collectively, this leads to cellular adaptations of protein synthesis, energy metabolism, mitochondrial respiration, lipid and carbon metabolism as well as nutrient acquisition. These mechanisms are integral inputs into fine- tuning the responses to hypoxic stress. Citation Format: M. Celeste Simon. Impact of oxygen and nutrient availability on sarcoma tumor neighborhood [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA017.